First session:
- Not heaps of paleo-specific R
- But building blocks to make you an expeRt
- Things that go into R (data inputs)
- How to structure your data inputs and outputs
- Getting started in R
26/06/2018
Pros and cons of the following:
githubScreenshot
Three principals:
note that we separate units of metadata with a "_" and within units, with a “-”.
This applies to scripts and data
e.g. function_clean-italics-tilia.R
example data screenshot
rstudio
getwd()
## [1] "/Users/Liv/Documents/paleo-R-workshop/1-folders-spreadsheets-organisingData"
setwd()
sessionInfo()
## R version 3.4.3 (2017-11-30) ## Platform: x86_64-apple-darwin15.6.0 (64-bit) ## Running under: macOS High Sierra 10.13.5 ## ## Matrix products: default ## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib ## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib ## ## locale: ## [1] en_NZ.UTF-8/en_NZ.UTF-8/en_NZ.UTF-8/C/en_NZ.UTF-8/en_NZ.UTF-8 ## ## attached base packages: ## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: ## [1] DiagrammeR_0.9.2 ## ## loaded via a namespace (and not attached): ## [1] Rcpp_0.12.16 highr_0.6 pillar_1.2.1 ## [4] compiler_3.4.3 RColorBrewer_1.1-2 influenceR_0.1.0 ## [7] plyr_1.8.4 bindr_0.1 viridis_0.4.0 ## [10] tools_3.4.3 digest_0.6.14 jsonlite_1.5 ## [13] viridisLite_0.2.0 gtable_0.2.0 evaluate_0.10.1 ## [16] tibble_1.4.2 rgexf_0.15.3 pkgconfig_2.0.1 ## [19] rlang_0.2.0 igraph_1.1.2 rstudioapi_0.7 ## [22] yaml_2.1.18 bindrcpp_0.2 gridExtra_2.3 ## [25] downloader_0.4 dplyr_0.7.4 stringr_1.3.0 ## [28] knitr_1.18 htmlwidgets_1.2 hms_0.4.2 ## [31] grid_3.4.3 rprojroot_1.2 glue_1.2.0 ## [34] R6_2.2.2 Rook_1.1-1 XML_3.98-1.9 ## [37] rmarkdown_1.9 ggplot2_2.2.1 purrr_0.2.4 ## [40] readr_1.1.1 tidyr_0.8.0 magrittr_1.5 ## [43] backports_1.1.1 scales_0.5.0 htmltools_0.3.6 ## [46] assertthat_0.2.0 colorspace_1.3-2 brew_1.0-6 ## [49] stringi_1.1.7 visNetwork_2.0.3 lazyeval_0.2.1 ## [52] munsell_0.4.3
require(tidyverse)
## Loading required package: tidyverse
## ── Attaching packages ──────────────────────────────────────────────────────── tidyverse 1.2.1 ──
## ✔ ggplot2 2.2.1 ✔ purrr 0.2.4 ## ✔ tibble 1.4.2 ✔ dplyr 0.7.4 ## ✔ tidyr 0.8.0 ✔ stringr 1.3.0 ## ✔ readr 1.1.1 ✔ forcats 0.3.0
## ── Conflicts ─────────────────────────────────────────────────────────── tidyverse_conflicts() ── ## ✖ dplyr::filter() masks stats::filter() ## ✖ dplyr::lag() masks stats::lag()
# install.packages("vegan")
# install.packages("skimr")
require(vegan)
require(skimr)
data("mite")
data("mite.env")
head(mite, n = 6)
| Brachy | PHTH | HPAV | RARD | SSTR | Protopl | MEGR | MPRO | TVIE | HMIN | HMIN2 | NPRA | TVEL | ONOV | SUCT | LCIL | Oribatl1 | Ceratoz1 | PWIL | Galumna1 | Stgncrs2 | HRUF | Trhypch1 | PPEL | NCOR | SLAT | FSET | Lepidzts | Eupelops | Miniglmn | LRUG | PLAG2 | Ceratoz3 | Oppiminu | Trimalc2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 17 | 5 | 5 | 3 | 2 | 1 | 4 | 2 | 2 | 1 | 4 | 1 | 17 | 4 | 9 | 50 | 3 | 1 | 1 | 8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 2 | 7 | 16 | 0 | 6 | 0 | 4 | 2 | 0 | 0 | 1 | 3 | 21 | 27 | 12 | 138 | 6 | 0 | 1 | 3 | 9 | 1 | 1 | 1 | 2 | 2 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 4 | 3 | 1 | 1 | 2 | 0 | 3 | 0 | 0 | 0 | 6 | 3 | 20 | 17 | 10 | 89 | 3 | 0 | 2 | 1 | 8 | 0 | 3 | 0 | 2 | 0 | 8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 23 | 7 | 10 | 2 | 2 | 0 | 4 | 0 | 1 | 2 | 10 | 0 | 18 | 47 | 17 | 108 | 10 | 1 | 0 | 1 | 2 | 1 | 2 | 1 | 3 | 2 | 12 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 5 | 8 | 13 | 9 | 0 | 13 | 0 | 0 | 0 | 3 | 14 | 3 | 32 | 43 | 27 | 5 | 1 | 0 | 5 | 2 | 1 | 0 | 1 | 0 | 0 | 0 | 12 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 19 | 7 | 5 | 9 | 3 | 2 | 3 | 0 | 0 | 20 | 16 | 2 | 13 | 38 | 39 | 3 | 5 | 0 | 1 | 1 | 8 | 0 | 4 | 0 | 1 | 0 | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
## Skim summary statistics ## n obs: 70 ## n variables: 35 ## ## ── Variable type:integer ──────────────────────────────────────────────────────────────────────── ## variable missing complete n mean sd p0 p25 p50 p75 p100 hist ## Brachy 0 70 70 8.73 10.08 0 3 4.5 11.75 42 ▇▂▁▂▁▁▁▁ ## Ceratoz1 0 70 70 1.29 1.46 0 0 1 2 5 ▇▆▁▃▁▁▁▁ ## Ceratoz3 0 70 70 1.3 2.2 0 0 0 2 9 ▇▁▁▁▁▁▁▁ ## Eupelops 0 70 70 0.64 0.99 0 0 0 1 4 ▇▃▁▁▁▁▁▁ ## FSET 0 70 70 1.86 3.18 0 0 0 2 12 ▇▂▁▁▁▁▁▁ ## Galumna1 0 70 70 0.96 1.73 0 0 0 1 8 ▇▁▁▁▁▁▁▁ ## HMIN 0 70 70 4.91 8.47 0 0 0 4.75 36 ▇▁▁▁▁▁▁▁ ## HMIN2 0 70 70 1.96 3.92 0 0 0 2.75 20 ▇▂▁▁▁▁▁▁ ## HPAV 0 70 70 8.51 7.56 0 4 6.5 12 37 ▇▇▃▃▁▁▁▁ ## HRUF 0 70 70 0.23 0.62 0 0 0 0 3 ▇▁▁▁▁▁▁▁ ## LCIL 0 70 70 35.26 88.85 0 1.25 13 44 723 ▇▁▁▁▁▁▁▁ ## Lepidzts 0 70 70 0.17 0.54 0 0 0 0 3 ▇▁▁▁▁▁▁▁ ## LRUG 0 70 70 10.43 12.66 0 0 4.5 17.75 57 ▇▂▂▁▁▁▁▁ ## MEGR 0 70 70 2.19 3.62 0 0 1 3 17 ▇▂▁▁▁▁▁▁ ## Miniglmn 0 70 70 0.24 0.79 0 0 0 0 5 ▇▁▁▁▁▁▁▁ ## MPRO 0 70 70 0.16 0.47 0 0 0 0 2 ▇▁▁▁▁▁▁▁ ## NCOR 0 70 70 1.13 1.65 0 0 0.5 1.75 7 ▇▃▂▂▁▁▁▁ ## NPRA 0 70 70 1.89 2.37 0 0 1 2.75 10 ▇▂▂▁▁▁▁▁ ## ONOV 0 70 70 17.27 18.05 0 5 10.5 24.25 73 ▇▃▂▁▁▁▁▁ ## Oppiminu 0 70 70 1.11 1.84 0 0 0 1.75 9 ▇▁▁▁▁▁▁▁ ## Oribatl1 0 70 70 1.89 3.43 0 0 0 2.75 17 ▇▁▁▁▁▁▁▁ ## PHTH 0 70 70 1.27 2.17 0 0 0 2 8 ▇▁▁▁▁▁▁▁ ## PLAG2 0 70 70 0.8 1.79 0 0 0 1 9 ▇▁▁▁▁▁▁▁ ## PPEL 0 70 70 0.17 0.54 0 0 0 0 3 ▇▁▁▁▁▁▁▁ ## Protopl 0 70 70 0.37 1.61 0 0 0 0 13 ▇▁▁▁▁▁▁▁ ## PWIL 0 70 70 1.09 1.71 0 0 0 1 8 ▇▁▁▁▁▁▁▁ ## RARD 0 70 70 1.21 2.78 0 0 0 1 13 ▇▂▁▁▁▁▁▁ ## SLAT 0 70 70 0.4 1.23 0 0 0 0 8 ▇▁▁▁▁▁▁▁ ## SSTR 0 70 70 0.31 0.97 0 0 0 0 6 ▇▁▁▁▁▁▁▁ ## Stgncrs2 0 70 70 0.73 1.83 0 0 0 0 9 ▇▁▁▁▁▁▁▁ ## SUCT 0 70 70 16.96 13.89 0 7.25 13.5 24 63 ▇▇▆▅▂▁▁▁ ## Trhypch1 0 70 70 2.61 6.14 0 0 0 2 29 ▇▁▁▁▁▁▁▁ ## Trimalc2 0 70 70 2.07 5.79 0 0 0 0 33 ▇▁▁▁▁▁▁▁ ## TVEL 0 70 70 9.06 10.93 0 0 3 19 42 ▇▁▁▂▁▁▁▁ ## TVIE 0 70 70 0.83 1.47 0 0 0 1 7 ▇▁▁▁▁▁▁▁